Posts Tagged ‘chair’

Halogen bonds 4: The strongest (?) halogen bond.

Sunday, December 7th, 2014

Continuing my hunt, here is a candidate for a strong(est?) halogen bond, this time between Se and I.[1].
The features of interest include:



  1. H. Maddox, and J.D. McCullough, " The Crystal and Molecular Structure of the Iodine Complex of 1-Oxa-4-selenacyclohexane, C 4 H 8 OSe.I 2 ", Inorganic Chemistry, vol. 5, pp. 522-526, 1966.

Ribulose-1,5-bisphosphate + carbon dioxide → carbon fixation!

Sunday, April 20th, 2014

Ribulose-1,5-bisphosphate reacts with carbon dioxide to produce 3-keto-2-carboxyarabinitol 1,5-bisphosphate as the first step in the biochemical process of carbon fixation. It needs an enzyme to do this (Ribulose-1,5-bisphosphate carboxylase/oxygenase, or RuBisCO) and lots of ATP (adenosine triphosphate, produced by photosynthesis). Here I ask what the nature of the uncatalysed transition state is, and hence the task that might be facing the catalyst in reducing the activation barrier to that of a facile thermal reaction. I present my process in the order it was done.


X-ray analysis and absolute configuration determination using porous complexes.

Wednesday, April 17th, 2013

This is another in the occasional series of “what a neat molecule”. In this case, more of a “what a neat idea”. The s-triazine below, when coordinated to eg ZnI2, forms what is called a metal-organic-framework, or MOF. A recent article[1] shows how such frameworks can be used to help solve a long-standing problem in structure determination, how to get a crystal structure on a compound that does not crystallise on its own.



  1. Y. Inokuma, S. Yoshioka, J. Ariyoshi, T. Arai, Y. Hitora, K. Takada, S. Matsunaga, K. Rissanen, and M. Fujita, "X-ray analysis on the nanogram to microgram scale using porous complexes", Nature, vol. 495, pp. 461-466, 2013.

Ring-flipping in cyclohexane in a different light

Friday, October 12th, 2012

The conformational analysis of cyclohexane is a mainstay of organic chemistry. Is there anything new that can be said about it? Let us start with the diagram below:


Updating a worked problem in conformational analysis. Part 1: the question.

Friday, May 13th, 2011

Conformational analysis comes from the classical renaissance of physical organic chemistry in the 1950s and 60s. The following problem is taken from E. D. Hughes and J. Wilby J. Chem. Soc., 1960, 4094-4101, DOI: 10.1039/JR9600004094, the essence of which is that Hofmann elimination of a neomenthyl derivative (C below) was observed as anomalously faster than its menthyl analogue. Of course, what is anomalous in one decade is a standard student problem (and one Nobel prize) five decades later.


The Cyclol Hypothesis for protein structure: castles in the air.

Monday, April 4th, 2011

Most scientific theories emerge slowly, over decades, but others emerge fully formed virtually overnight as it were (think  Einstein in 1905). A third category is the supernova type, burning brightly for a short while, but then vanishing (almost) without trace shortly thereafter. The structure of DNA (of which I have blogged elsewhere) belongs to the second class, whilst one the brightest (and now entirely forgotten) examples of the supernova type concerns the structure of proteins. In 1936, it must have seemed a sure bet that the first person to come up with a successful theory of the origins of the (non-random) relatively rigid structure of proteins would inevitably win a Nobel prize (and of course this did happen for that other biologically important system, DNA, some 17 years later). Compelling structures for larger molecules providing reliable atom-atom distances based on crystallography were still in the future in 1936, and so structural theories contained a fair element of speculation and hopefully inspired guesswork (much as cosmological theories appear to have nowadays!).


Semantically rich molecules

Sunday, May 2nd, 2010

Peter Murray-Rust in his blog asks for examples of the Scientific Semantic Web, a topic we have both been banging on about for ten years or more (DOI: 10.1021/ci000406v). What we are seeking of course is an example of how scientific connections have been made using inference logic from semantically rich statements to be found on the Web (ideally connections that might not have previously been spotted by humans, and lie overlooked and unloved in the scientific literature). Its a tough cookie, and I look forward to the examples that Peter identifies. Meanwhile, I thought I might share here a semantically rich molecule. OK, I identified this as such not by using the Web, but as someone who is in the process of delivering an undergraduate lecture course on the topic of conformational analysis. This course takes the form of presenting a set of rules or principles which relate to the conformations of molecules, and which themselves derive from quantum mechanics, and then illustrating them with selected annotated examples. To do this, a great many semantic connections have to be made, and in the current state of play, only a human can really hope to make most of these. We really look to the semantic web as it currently is to perhaps spot a few connections that might have been overlooked in this process. So, below is a molecule, and I have made a few semantic connections for it (but have not actually fully formalised them in this blog; that is a different topic I might return to at some time). I feel in my bones that more connections could be made, and offer the molecule here as the fuse!


Conformational analysis of cyclotriborazane

Sunday, February 14th, 2010

In an earlier post, I re-visited the conformational analysis of cyclohexane by looking at the vibrations of the entirely planar form (of D6h symmetry). The method also gave interesting results for the larger cyclo-octane ring. How about a larger leap into the unknown?


The conformation of cyclohexane

Thursday, January 28th, 2010

Like benzene, its fully saturated version cyclohexane represents an icon of organic chemistry. By 1890, the structure of planar benzene was pretty much understood, but organic chemistry was still struggling somewhat to fully embrace three rather than two dimensions. A grand-old-man of organic chemistry at the time, Adolf von Baeyer, believed that cyclohexane too was flat, and what he said went. So when a young upstart named Hermann Sachse suggested it was not flat, and furthermore could exist in two forms, which we now call chair and boat, no-one believed him. His was a trigonometric proof, deriving from the tetrahedral angle of 109.47 at carbon, and producing what he termed strainless rings.


Conformational analysis and enzyme activity: models for amide hydrolysis.

Sunday, April 12th, 2009

The diagram below summarizes an interesting result recently reported by Hanson and co-workers (DOI: 10.1021/jo800706y. At ~neutral pH, compound 13 hydrolyses with a half life of 21 minutes, whereas 14 takes 840 minutes. Understanding this difference in reactivity may allow us to understand why some enzymes can catalyze the hydrolysis of peptides with an acceleration of up to twelve orders of magnitude.